MolNFT v1 · #50121 · protein

Crystal structure of yrbi phosphatase from escherichia COLI in complex with a phosphate and a calcium ion

2R8Z · 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase: “Crystal structure of yrbi phosphatase from escherichia COLI in complex with a phosphate and a calcium ion”. X-ray diffraction, 2 ligands (CA, PO4), 20 pockets (best druggability…

PDB: 2R8Z
Type: protein
Length: 2,890 residues
Chains: 16
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase
EC: 3.1.3.45
UniProt: P67653
Ligands: CA, PO4
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, F, G, H, I, J, K, L, M, N, P	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45)	protein	181	36% helix, 19% strand	P67653
E, O	3-deoxy-D-manno-octulosonate 8-phosphate phosphatase (EC 3.1.3.45)	protein	178	37% helix, 19% strand	P67653

Ligands and binding sites

CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, H, F, G, I, L, J, K, M, N, O, P
PO4 · Phosphate ion · ion · 16 copies · chains A, D, B, C, E, H, F, G, I, L, J, K, M, N, O, P

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1134	0.79	0.81	100	PO4
2	1061	0.72	0.75	97	empty
3	494	0.66	0.77	53	empty
4	318	0.65	0.80	29	CA, PO4
5	593	0.65	0.75	54	empty

Interfaces

36 interfaces between chains.

B–C · 1190 Å² buried · 22 hydrogen bonds · protein-protein
I–J · 1181 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 1179 Å² buried · 22 hydrogen bonds · protein-protein
E–H · 1179 Å² buried · 20 hydrogen bonds · protein-protein
A–B · 1174 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

2R8Z · Crystal structure of YrbI phosphatase from Escherichia coli in complex with a phosphate… · the same entry in another collection · chain M against M, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P67653
Elsewhere: RCSB PDB 2R8Z · PDBe 2R8Z · UniProt P67653

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